Speaker
Description
Ribosome is a huge biomolecular complex responsible for protein synthesis in all living organisms. As a multi-component system consisting of several strands of RNA and a few dozen proteins, the ribosome is particularly challenging for current molecular dynamics simulations [1]. In the past few years, we carried out many atomistic computer simulations of the entire ribosome in explicit aqueous environment to better understand how nascent proteins emerge through the ribosome exit tunnel to the cytosol. We have learned that the tunnel offers a unique conditions to form a secondary structure of certain nascent protein sequences causing translational arrest [2]. We studied how the information about ribosome surface is transferred to its interior [3]. Most recently we have described the structure and dynamics of the narrowest part of the ribosome exit tunnel, the function of which has remained under debate for decades. The talk will summarize our simulation efforts to understand the ribosome as a crucial player in the life as we know it.
- Bock LV, Kolář MH, Grubmüller H, Curr. Opin. Struct. Biol. 2018, DOI: 10.1016/j.sbi.2017.11.003
- Kolář MH et al. Nucl. Acids Res. 2022, DOI: 10.1093/nar/gkac038
- McGrath H, Černeková M, Kolář MH, biorxiv.org 2022,\ DOI: 10.1101/2022.04.20.488877
